Assailants whipped, clubbed and sexually assaulted the victims after they walked to a food distribution center, the relief organization said.
The attacks occurred between Nov. 19 and Thursday, it said on Saturday.
A midwife with the group who treated some survivors said those who were targeted included pregnant and elderly women and girls as young as 10.
"What is happening since last week is indescribable. I haven’t got words for it," Ruth Okello said.
She said the women also were robbed of clothing and shoes, and their ration cards for food distribution were seized and destroyed.
Sexual violence has been widespread during the civil war in South Sudan.
Despite a recent peace deal, aid workers have warned of higher rates of sexual assault as growing numbers of desperate people try to reach aid.